Apatite layers were grown on the surface of newly developed starch/polycaprolactone (SPCL)-based scaffolds by a 3D plotting technology. To produce the biomimetic coatings, a sodium silicate gel was used as nucleating agent, followed by immersion in a simulated body fluid (SBF) solution. After growing a stable apatite layer for 7 days, the scaffolds were placed in SBF under static, agitated (80 strokes min−1) and circulating flow perfusion (Q = 4 ml min−1; tR = 15 s) for up to 14 days. The materials were characterized by scanning electron microscopy/energy dispersive X-ray spectroscopy, Fourier transform infrared spectroscopy and thin-film X-ray diffraction. Cross-sections were obtained and the coating thickness was measured. The elemental composition of solution and coatings was monitored by inductively coupled plasma spectroscopy. After only 6 h of immersion in SBF it was possible to observe the formation of small nuclei of an amorphous calcium phosphate (ACP) layer. After subsequent SBF immersion from 7 to 14 days under static, agitated and circulating flow perfusion conditions, these layers grew into bone-like nanocrystalline carbonated apatites covering each scaffold fiber without compromising its initial morphology. No differences in the apatite composition/chemical structure were detectable between the coating conditions. In case of flow perfusion, the coating thickness was significantly higher. This condition, besides mimicking better the biological milieu, allowed for the coating of complex architectures at higher rates, which can greatly reduce the coating step.